Science Gateways Listing

Proteogenomics Gateway

Pratik Jagtap
Field of Science
Biochemistry and Molecular Structure and Function
Relevant Link(s)
Portal Homepage More Information
Additional Contact(s)
Timothy Griffin Pratik Jagtap Matthew Chambers

Description: This page provides links to instructional materials describing how to access and use the proteogenomic workflows described in the manuscript text. Please access the links indicated below for the following materials: Training on How to access and use the training site: Interactive Galaxy Tours Accessing an interactive Galaxy Tour describing the RNA-seq-to-protein-database workflow: Accessing an interactive Galaxy Tour describing Dataset Collections: Accessing an interactive Galaxy Tour describing the protein sequence database search workflow: Workflow training and operation Instructions on running the RNA-seq-to-protein-database workflow: Instructions on running the protein sequence database search workflow and interpreting results: JetStream instance Instructions for accessing workflows on the JetStream Galaxy instance:

Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry–based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics. Our resource brings together software from several leading research groups to address two foundational aspects of proteogenomics: (i) generation of customized, annotated protein sequence databases from RNA-Seq data; and (ii) accurate matching of tandem mass spectrometry data to putative variants, followed by filtering to confirm their novelty. Directions for accessing software tools and workflows, along with instructional documentation, can be found at